I am sorry but there is no magical voodoo in MasterPages. It all comes out as HTML.
So if one works and one doesn't then that means that the output is different.
The sample that you gave me is a known CSS bug with Microsoft Tables and speciying 100% width on elements that are not one 100% width because of the way that the tables are calculated/rendered.
I asked for multiple versions because if you had a version that works and a version that did not work then i could see the differences. Initially i thought it was the div but that does not appear to be it.
If you have 1 working version and a non-working version I want to see the output. You can also provide the input required to create both.
this means
Masterpage markup
COntentpage markup
Full page markup
---------------------------
HTML Output of masterpage output
HTML Output of full page